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Example of generating configuration files for pheniqs 2.0 for packing fastq to CRAM
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#!/usr/bin/env python3 | |
# -*- coding: utf-8 -*- | |
import io | |
import os | |
import re | |
import sys | |
import json | |
import logging | |
from datetime import date | |
inode_type = lambda path: ( os.path.isfile(path) and 'file' ) or 'directory' | |
def to_json(node): | |
return json.dumps(node, sort_keys=True, ensure_ascii=False, indent=4) | |
class Scanner(object): | |
def __init__(self, ontology): | |
self.log = logging.getLogger('Scanner') | |
self.ontology = ontology | |
self.inode = [] | |
@property | |
def expression(self): | |
return self.ontology['expression'] | |
def search(self): | |
def collect(path, recursive, depth=1): | |
result = [] | |
# The path might actually not exist, for instance a dangling symlink | |
if os.path.exists(path): | |
decoded = { | |
'path': path, | |
'inode type': inode_type(path), | |
'dirname': os.path.dirname(path), | |
'basename': os.path.basename(path), | |
} | |
if decoded['inode type'] == 'directory': | |
if (recursive or depth > 0): | |
# recursively scan decedent paths | |
for next in os.listdir(decoded['path']): | |
next = os.path.abspath(os.path.join(decoded['path'],next)) | |
result.extend(collect(next, recursive, depth - 1)) | |
self.log.debug('considering %d inodes in %s', len(result), decoded['path']) | |
else: | |
match = self.expression.search(decoded['basename']) | |
if match: | |
for k,v in match.groupdict().items(): | |
if k in [ | |
'day', | |
'month', | |
'year', | |
'lane_number', | |
'segment_number' | |
]: | |
decoded[k] = int(v) | |
else: | |
decoded[k] = v | |
if 'year' in decoded: | |
decoded['year'] += 2000 | |
if all(i in decoded for i in ('day', 'month', 'year')): | |
decoded['iso date'] = date(**dict([(i,decoded[i]) for i in ('day', 'month', 'year')])).isoformat() | |
result.append(decoded) | |
else: | |
self.log.debug('ignoring non exiting path %s', path) | |
return result | |
self.inode = [] | |
if self.ontology['scan path']: | |
for path in self.ontology['scan path']: | |
if os.path.exists(path): | |
path = os.path.abspath(os.path.expanduser(os.path.expandvars(path))) | |
self.inode.extend(collect(path, self.ontology['recursive'])) | |
else: | |
self.log.error('path %s does not exist', path) | |
self.log.info('%d locations resolved in %s', len(self.inode), ' '.join(self.ontology['scan path'])) | |
def sort_by_library(inode_array): | |
inode_by_library = {} | |
for inode in inode_array: | |
if 'library' in inode: | |
if inode['library'] not in inode_by_library: | |
inode_by_library[inode['library']] = [] | |
inode_by_library[inode['library']].append(inode) | |
for library in inode_by_library.keys(): | |
inode_by_library[library] = sorted(inode_by_library[library], key=lambda o: o['segment_number']) | |
return inode_by_library | |
def sort_by_trimmed_library(inode_array): | |
inode_by_trimmed_library = {} | |
for inode in inode_array: | |
if 'library' in inode: | |
if inode['library'] not in inode_by_trimmed_library: | |
inode_by_trimmed_library[inode['library']] = { | |
'PE': [], | |
'1SE': [], | |
'2SE': [] | |
} | |
if inode['trimmed_group'] == 'PE': | |
inode_by_trimmed_library[inode['library']]['PE'].append(inode) | |
elif inode['trimmed_group'] == 'SE': | |
if inode['segment_number'] == 1: | |
inode_by_trimmed_library[inode['library']]['1SE'].append(inode) | |
elif inode['segment_number'] == 2: | |
inode_by_trimmed_library[inode['library']]['2SE'].append(inode) | |
for library in inode_by_trimmed_library.keys(): | |
for group in ['PE', '1SE', '2SE']: | |
inode_by_trimmed_library[library][group] = sorted(inode_by_trimmed_library[library][group], key=lambda o: o['segment_number']) | |
return inode_by_trimmed_library | |
def main(): | |
logging.basicConfig() | |
logging.getLogger().setLevel(logging.DEBUG) | |
# example file name HJWKJCCXX_2_151215_FR05811676_Homo-sapiens__R_151215_YOUIDA_M001_R1.fastq.gz | |
# Bellow is my educated guess for the metadata encoded in the file name, i might be wrong about some | |
# I am going to assume a single _ is used as separator | |
# HJWKJCCXX : flowcell id | |
# 2 : lane number | |
# 151215 : run date in < day >< month >< year > format | |
# FR05811676 : Library, I will assume this is the unique key we to aggregate segments for | |
# Homo-sapiens : species | |
# _R : Not sure what this is | |
# 151215 : The run date again | |
# YOUIDA : Not sure about this, is this part of the library name? | |
# M001 : part of the illumina flowcell geometry naming scheme, probably redundant | |
# R1 : segment number prefixed by the letter R | |
# .fastq.gz : compressed fastq text file | |
raw = Scanner({ | |
'recursive': False, | |
'scan path': [ 'example' ], | |
'expression': re.compile ( | |
r'^{}\.fastq\.gz$'.format ( | |
r'_'.join ( | |
[ | |
r'(?P<flowcell_id>[^_]+)', | |
r'(?P<lane_number>[0-9])', | |
r'(?P<day>[0-9]{2})(?P<month>[0-9]{2})(?P<year>[0-9]{2})', | |
r'(?P<library>[^_]+)', | |
r'(?P<species>[^_]+)', | |
r'(?:_R)', | |
r'(?:[0-9]{6})', | |
r'(?:[^_]+)', | |
r'(?:M[0-9]{3})', | |
r'R(?P<segment_number>[0-9]+)', | |
] | |
) | |
) | |
) | |
}) | |
raw.search() | |
inode_by_library = sort_by_library(raw.inode) | |
instruction_array =[] | |
for k, v in inode_by_library.items(): | |
lead = v[0] | |
instruction = { | |
'PL': 'ILLUMINA', | |
'DT': lead['iso date'], | |
'flowcell id': lead['flowcell_id'], | |
'flowcell lane number': lead['lane_number'], | |
'multiplex': { | |
'undetermined': { | |
'LB': lead['library'], | |
'output': [ | |
'{}_l0{}_{}.cram'.format(lead['flowcell_id'], str(lead['lane_number']), lead['library']) | |
] | |
} | |
} | |
} | |
base_input = os.path.commonpath([i['dirname'] for i in v]) | |
if base_input: | |
instruction['base input url'] = base_input | |
instruction['input'] = [os.path.relpath(i['path'], base_input) for i in v] | |
else: | |
instruction['input'] = [i['path'] for i in v] | |
instruction_array.append(instruction) | |
# print(to_json(inode_by_library)) | |
# 151215_FR05811634_read1_trimmomatic_1PE.fastq.gz; | |
# 151215_FR05811634_read2_trimmomatic_2PE.fastq.gz; | |
# 151215_FR05811634_read1_trimmomatic_1SE.fastq.gz; | |
# 151215_FR05811634_read2_trimmomatic_2SE.fastq.gz; | |
# | |
# 151215 : run date in < day >< month >< year > format | |
# FR05811634 : Library, I will assume this is the unique key we to aggregate segments for | |
# read1 : segment 1 of the read | |
# trimmomatic : not really informative | |
# (1|2)(PE|SE) : the first integer is actually redundant since we already encoded the segment number and second is a trim group | |
# .fastq.gz : compressed fastq text file | |
raw = Scanner({ | |
'recursive': True, | |
'scan path': [ 'example/TRIMMED' ], | |
'expression': re.compile ( | |
r'^{}\.fastq\.gz$'.format ( | |
r'_'.join ( | |
[ | |
r'(?P<day>[0-9]{2})(?P<month>[0-9]{2})(?P<year>[0-9]{2})', | |
r'(?P<library>[^_]+)', | |
r'read(?P<segment_number>[0-9]+)', | |
r'(?:trimmomatic)', | |
r'[0-9]+(?P<trimmed_group>PE|SE)', | |
] | |
) | |
) | |
) | |
}) | |
raw.search() | |
inode_by_trimmed_library = sort_by_trimmed_library(raw.inode) | |
for library in inode_by_trimmed_library.values(): | |
for group in library.values(): | |
lead = group[0] | |
instruction = { | |
'PL': 'ILLUMINA', | |
'DT': lead['iso date'], | |
'multiplex': { | |
'undetermined': { | |
'LB': lead['library'], | |
'output': [] | |
} | |
} | |
} | |
if 'flowcell_id' in lead: | |
instruction['flowcell id'] = lead['flowcell_id'] | |
if 'lane_number' in lead: | |
instruction['flowcell lane number'] = lead['lane_number'] | |
base_input = os.path.commonpath([i['dirname'] for i in group]) | |
if base_input: | |
instruction['base input url'] = base_input | |
instruction['input'] = [os.path.relpath(i['path'], base_input) for i in group] | |
else: | |
instruction['input'] = [i['path'] for i in group] | |
if lead['trimmed_group'] == 'SE': | |
instruction['multiplex']['undetermined']['output'].append ( | |
'{}_trimmed_SE{}.cram'.format(lead['library'], str(lead['segment_number'])) | |
) | |
else: | |
instruction['multiplex']['undetermined']['output'].append ( | |
'{}_trimmed_PE.cram'.format(lead['library']) | |
) | |
instruction_array.append(instruction) | |
# print(to_json(inode_by_trimmed_library)) | |
print(to_json(instruction_array)) | |
sys.exit(0) | |
if __name__ == '__main__': | |
main() |
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[ | |
{ | |
"DT": "2015-12-15", | |
"PL": "ILLUMINA", | |
"base input url": "/Users/lg/Desktop/vinu/example", | |
"flowcell id": "HKJWVCCXX", | |
"flowcell lane number": 8, | |
"input": [ | |
"HKJWVCCXX_8_151215_FR05811644_Homo-sapiens__R_151215_YOUIDA_M001_R1.fastq.gz", | |
"HKJWVCCXX_8_151215_FR05811644_Homo-sapiens__R_151215_YOUIDA_M001_R2.fastq.gz" | |
], | |
"multiplex": { | |
"undetermined": { | |
"LB": "FR05811644", | |
"output": [ | |
"HKJWVCCXX_l08_FR05811644.cram" | |
] | |
} | |
} | |
}, | |
{ | |
"DT": "2015-12-15", | |
"PL": "ILLUMINA", | |
"base input url": "/Users/lg/Desktop/vinu/example", | |
"flowcell id": "HKJHJCCXX", | |
"flowcell lane number": 3, | |
"input": [ | |
"HKJHJCCXX_3_151215_FR05811658_Homo-sapiens__R_151215_YOUIDA_M001_R1.fastq.gz", | |
"HKJHJCCXX_3_151215_FR05811658_Homo-sapiens__R_151215_YOUIDA_M001_R2.fastq.gz" | |
], | |
"multiplex": { | |
"undetermined": { | |
"LB": "FR05811658", | |
"output": [ | |
"HKJHJCCXX_l03_FR05811658.cram" | |
] | |
} | |
} | |
}, | |
{ | |
"DT": "2015-12-15", | |
"PL": "ILLUMINA", | |
"base input url": "/Users/lg/Desktop/vinu/example", | |
"flowcell id": "HKJHJCCXX", | |
"flowcell lane number": 6, | |
"input": [ | |
"HKJHJCCXX_6_151215_FR05811666_Homo-sapiens__R_151215_YOUIDA_M001_R1.fastq.gz", | |
"HKJHJCCXX_6_151215_FR05811666_Homo-sapiens__R_151215_YOUIDA_M001_R2.fastq.gz" | |
], | |
"multiplex": { | |
"undetermined": { | |
"LB": "FR05811666", | |
"output": [ | |
"HKJHJCCXX_l06_FR05811666.cram" | |
] | |
} | |
} | |
}, | |
{ | |
"DT": "2015-12-15", | |
"PL": "ILLUMINA", | |
"base input url": "/Users/lg/Desktop/vinu/example", | |
"flowcell id": "HJWKJCCXX", | |
"flowcell lane number": 2, | |
"input": [ | |
"HJWKJCCXX_2_151215_FR05811676_Homo-sapiens__R_151215_YOUIDA_M001_R1.fastq.gz", | |
"HJWKJCCXX_2_151215_FR05811676_Homo-sapiens__R_151215_YOUIDA_M001_R2.fastq.gz" | |
], | |
"multiplex": { | |
"undetermined": { | |
"LB": "FR05811676", | |
"output": [ | |
"HJWKJCCXX_l02_FR05811676.cram" | |
] | |
} | |
} | |
}, | |
{ | |
"DT": "2015-12-15", | |
"PL": "ILLUMINA", | |
"base input url": "/Users/lg/Desktop/vinu/example", | |
"flowcell id": "HK7YCCCXX", | |
"flowcell lane number": 4, | |
"input": [ | |
"HK7YCCCXX_4_151215_FR05811634_Homo-sapiens__R_151215_YOUIDA_M001_R1.fastq.gz", | |
"HK7YCCCXX_4_151215_FR05811634_Homo-sapiens__R_151215_YOUIDA_M001_R2.fastq.gz" | |
], | |
"multiplex": { | |
"undetermined": { | |
"LB": "FR05811634", | |
"output": [ | |
"HK7YCCCXX_l04_FR05811634.cram" | |
] | |
} | |
} | |
}, | |
{ | |
"DT": "2015-12-15", | |
"PL": "ILLUMINA", | |
"base input url": "/Users/lg/Desktop/vinu/example", | |
"flowcell id": "HKJHJCCXX", | |
"flowcell lane number": 2, | |
"input": [ | |
"HKJHJCCXX_2_151215_FR05811652_Homo-sapiens__R_151215_YOUIDA_M001_R1.fastq.gz", | |
"HKJHJCCXX_2_151215_FR05811652_Homo-sapiens__R_151215_YOUIDA_M001_R2.fastq.gz" | |
], | |
"multiplex": { | |
"undetermined": { | |
"LB": "FR05811652", | |
"output": [ | |
"HKJHJCCXX_l02_FR05811652.cram" | |
] | |
} | |
} | |
}, | |
{ | |
"DT": "2015-12-15", | |
"PL": "ILLUMINA", | |
"base input url": "/Users/lg/Desktop/vinu/example", | |
"flowcell id": "HKJHJCCXX", | |
"flowcell lane number": 4, | |
"input": [ | |
"HKJHJCCXX_4_151215_FR05811659_Homo-sapiens__R_151215_YOUIDA_M001_R1.fastq.gz", | |
"HKJHJCCXX_4_151215_FR05811659_Homo-sapiens__R_151215_YOUIDA_M001_R2.fastq.gz" | |
], | |
"multiplex": { | |
"undetermined": { | |
"LB": "FR05811659", | |
"output": [ | |
"HKJHJCCXX_l04_FR05811659.cram" | |
] | |
} | |
} | |
}, | |
{ | |
"DT": "2015-12-15", | |
"PL": "ILLUMINA", | |
"base input url": "/Users/lg/Desktop/vinu/example", | |
"flowcell id": "HKJWVCCXX", | |
"flowcell lane number": 5, | |
"input": [ | |
"HKJWVCCXX_5_151215_FR05811636_Homo-sapiens__R_151215_YOUIDA_M001_R1.fastq.gz", | |
"HKJWVCCXX_5_151215_FR05811636_Homo-sapiens__R_151215_YOUIDA_M001_R2.fastq.gz" | |
], | |
"multiplex": { | |
"undetermined": { | |
"LB": "FR05811636", | |
"output": [ | |
"HKJWVCCXX_l05_FR05811636.cram" | |
] | |
} | |
} | |
}, | |
{ | |
"DT": "2015-12-15", | |
"PL": "ILLUMINA", | |
"base input url": "/Users/lg/Desktop/vinu/example", | |
"flowcell id": "HKJHJCCXX", | |
"flowcell lane number": 1, | |
"input": [ | |
"HKJHJCCXX_1_151215_FR05811674_Homo-sapiens__R_151215_YOUIDA_M001_R1.fastq.gz", | |
"HKJHJCCXX_1_151215_FR05811674_Homo-sapiens__R_151215_YOUIDA_M001_R2.fastq.gz" | |
], | |
"multiplex": { | |
"undetermined": { | |
"LB": "FR05811674", | |
"output": [ | |
"HKJHJCCXX_l01_FR05811674.cram" | |
] | |
} | |
} | |
}, | |
{ | |
"DT": "2015-12-15", | |
"PL": "ILLUMINA", | |
"base input url": "/Users/lg/Desktop/vinu/example", | |
"flowcell id": "HKJHJCCXX", | |
"flowcell lane number": 7, | |
"input": [ | |
"HKJHJCCXX_7_151215_FR05811667_Homo-sapiens__R_151215_YOUIDA_M001_R1.fastq.gz", | |
"HKJHJCCXX_7_151215_FR05811667_Homo-sapiens__R_151215_YOUIDA_M001_R2.fastq.gz" | |
], | |
"multiplex": { | |
"undetermined": { | |
"LB": "FR05811667", | |
"output": [ | |
"HKJHJCCXX_l07_FR05811667.cram" | |
] | |
} | |
} | |
}, | |
{ | |
"DT": "2015-12-15", | |
"PL": "ILLUMINA", | |
"base input url": "/Users/lg/Desktop/vinu/example", | |
"flowcell id": "HJWKJCCXX", | |
"flowcell lane number": 4, | |
"input": [ | |
"HJWKJCCXX_4_151215_FR05811683_Homo-sapiens__R_151215_YOUIDA_M001_R1.fastq.gz", | |
"HJWKJCCXX_4_151215_FR05811683_Homo-sapiens__R_151215_YOUIDA_M001_R2.fastq.gz" | |
], | |
"multiplex": { | |
"undetermined": { | |
"LB": "FR05811683", | |
"output": [ | |
"HJWKJCCXX_l04_FR05811683.cram" | |
] | |
} | |
} | |
}, | |
{ | |
"DT": "2015-12-15", | |
"PL": "ILLUMINA", | |
"base input url": "/Users/lg/Desktop/vinu/example", | |
"flowcell id": "HKJWVCCXX", | |
"flowcell lane number": 4, | |
"input": [ | |
"HKJWVCCXX_4_151215_FR05811651_Homo-sapiens__R_151215_YOUIDA_M001_R1.fastq.gz", | |
"HKJWVCCXX_4_151215_FR05811651_Homo-sapiens__R_151215_YOUIDA_M001_R2.fastq.gz" | |
], | |
"multiplex": { | |
"undetermined": { | |
"LB": "FR05811651", | |
"output": [ | |
"HKJWVCCXX_l04_FR05811651.cram" | |
] | |
} | |
} | |
}, | |
{ | |
"DT": "2015-12-15", | |
"PL": "ILLUMINA", | |
"base input url": "/Users/lg/Desktop/vinu/example", | |
"flowcell id": "HK7YCCCXX", | |
"flowcell lane number": 5, | |
"input": [ | |
"HK7YCCCXX_5_151215_FR05811650_Homo-sapiens__R_151215_YOUIDA_M001_R1.fastq.gz", | |
"HK7YCCCXX_5_151215_FR05811650_Homo-sapiens__R_151215_YOUIDA_M001_R2.fastq.gz" | |
], | |
"multiplex": { | |
"undetermined": { | |
"LB": "FR05811650", | |
"output": [ | |
"HK7YCCCXX_l05_FR05811650.cram" | |
] | |
} | |
} | |
}, | |
{ | |
"DT": "2015-12-15", | |
"PL": "ILLUMINA", | |
"base input url": "/Users/lg/Desktop/vinu/example", | |
"flowcell id": "HKJHJCCXX", | |
"flowcell lane number": 5, | |
"input": [ | |
"HKJHJCCXX_5_151215_FR05811660_Homo-sapiens__R_151215_YOUIDA_M001_R1.fastq.gz", | |
"HKJHJCCXX_5_151215_FR05811660_Homo-sapiens__R_151215_YOUIDA_M001_R2.fastq.gz" | |
], | |
"multiplex": { | |
"undetermined": { | |
"LB": "FR05811660", | |
"output": [ | |
"HKJHJCCXX_l05_FR05811660.cram" | |
] | |
} | |
} | |
}, | |
{ | |
"DT": "2015-12-15", | |
"PL": "ILLUMINA", | |
"base input url": "/Users/lg/Desktop/vinu/example", | |
"flowcell id": "HKJWVCCXX", | |
"flowcell lane number": 7, | |
"input": [ | |
"HKJWVCCXX_7_151215_FR05811643_Homo-sapiens__R_151215_YOUIDA_M001_R1.fastq.gz", | |
"HKJWVCCXX_7_151215_FR05811643_Homo-sapiens__R_151215_YOUIDA_M001_R2.fastq.gz" | |
], | |
"multiplex": { | |
"undetermined": { | |
"LB": "FR05811643", | |
"output": [ | |
"HKJWVCCXX_l07_FR05811643.cram" | |
] | |
} | |
} | |
}, | |
{ | |
"DT": "2015-12-15", | |
"PL": "ILLUMINA", | |
"base input url": "/Users/lg/Desktop/vinu/example", | |
"flowcell id": "HKK7VCCXX", | |
"flowcell lane number": 5, | |
"input": [ | |
"HKK7VCCXX_5_151215_FR05811635_Homo-sapiens__R_151215_YOUIDA_M001_R1.fastq.gz", | |
"HKK7VCCXX_5_151215_FR05811635_Homo-sapiens__R_151215_YOUIDA_M001_R2.fastq.gz" | |
], | |
"multiplex": { | |
"undetermined": { | |
"LB": "FR05811635", | |
"output": [ | |
"HKK7VCCXX_l05_FR05811635.cram" | |
] | |
} | |
} | |
}, | |
{ | |
"DT": "2015-12-15", | |
"PL": "ILLUMINA", | |
"base input url": "/Users/lg/Desktop/vinu/example", | |
"flowcell id": "HKJHJCCXX", | |
"flowcell lane number": 8, | |
"input": [ | |
"HKJHJCCXX_8_151215_FR05811668_Homo-sapiens__R_151215_YOUIDA_M001_R1.fastq.gz", | |
"HKJHJCCXX_8_151215_FR05811668_Homo-sapiens__R_151215_YOUIDA_M001_R2.fastq.gz" | |
], | |
"multiplex": { | |
"undetermined": { | |
"LB": "FR05811668", | |
"output": [ | |
"HKJHJCCXX_l08_FR05811668.cram" | |
] | |
} | |
} | |
}, | |
{ | |
"DT": "2015-12-15", | |
"PL": "ILLUMINA", | |
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{ | |
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{ | |
"DT": "2015-12-15", | |
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"base input url": "/Users/lg/Desktop/vinu/example", | |
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{ | |
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} | |
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{ | |
"DT": "2015-12-15", | |
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] | |
} | |
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{ | |
"DT": "2015-12-15", | |
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] | |
} | |
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{ | |
"DT": "2015-12-15", | |
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"LB": "FR05811668", | |
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} | |
} | |
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{ | |
"DT": "2015-12-15", | |
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] | |
} | |
} | |
}, | |
{ | |
"DT": "2015-12-15", | |
"PL": "ILLUMINA", | |
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] | |
} | |
} | |
}, | |
{ | |
"DT": "2015-12-15", | |
"PL": "ILLUMINA", | |
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} | |
} | |
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{ | |
"DT": "2015-12-15", | |
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} | |
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{ | |
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] | |
} | |
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{ | |
"DT": "2015-12-15", | |
"PL": "ILLUMINA", | |
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} | |
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{ | |
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] | |
} | |
} | |
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{ | |
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] | |
} | |
} | |
}, | |
{ | |
"DT": "2015-12-15", | |
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] | |
} | |
} | |
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{ | |
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] | |
} | |
} | |
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{ | |
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"LB": "FR05811667", | |
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] | |
} | |
} | |
}, | |
{ | |
"DT": "2015-12-15", | |
"PL": "ILLUMINA", | |
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} | |
} | |
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{ | |
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} | |
} | |
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{ | |
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] | |
} | |
} | |
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{ | |
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} | |
} | |
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{ | |
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} | |
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{ | |
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] | |
} | |
} | |
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{ | |
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} | |
} | |
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{ | |
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} | |
} | |
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{ | |
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] | |
} | |
} | |
}, | |
{ | |
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"PL": "ILLUMINA", | |
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] | |
} | |
} | |
}, | |
{ | |
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] | |
} | |
} | |
}, | |
{ | |
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] | |
} | |
} | |
}, | |
{ | |
"DT": "2015-12-15", | |
"PL": "ILLUMINA", | |
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] | |
} | |
} | |
}, | |
{ | |
"DT": "2015-12-15", | |
"PL": "ILLUMINA", | |
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] | |
} | |
} | |
}, | |
{ | |
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"PL": "ILLUMINA", | |
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"output": [ | |
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] | |
} | |
} | |
}, | |
{ | |
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] | |
} | |
} | |
}, | |
{ | |
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"output": [ | |
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] | |
} | |
} | |
}, | |
{ | |
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], | |
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"LB": "FR05811684", | |
"output": [ | |
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] | |
} | |
} | |
}, | |
{ | |
"DT": "2015-12-15", | |
"PL": "ILLUMINA", | |
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], | |
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"output": [ | |
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] | |
} | |
} | |
}, | |
{ | |
"DT": "2015-12-15", | |
"PL": "ILLUMINA", | |
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"input": [ | |
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], | |
"multiplex": { | |
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"LB": "FR05811660", | |
"output": [ | |
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] | |
} | |
} | |
}, | |
{ | |
"DT": "2015-12-15", | |
"PL": "ILLUMINA", | |
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"input": [ | |
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], | |
"multiplex": { | |
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"LB": "FR05811660", | |
"output": [ | |
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] | |
} | |
} | |
}, | |
{ | |
"DT": "2015-12-15", | |
"PL": "ILLUMINA", | |
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"151215_FR05811652_read2_trimmomatic_2PE.fastq.gz" | |
], | |
"multiplex": { | |
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"LB": "FR05811652", | |
"output": [ | |
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] | |
} | |
} | |
}, | |
{ | |
"DT": "2015-12-15", | |
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"input": [ | |
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], | |
"multiplex": { | |
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"LB": "FR05811652", | |
"output": [ | |
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] | |
} | |
} | |
}, | |
{ | |
"DT": "2015-12-15", | |
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"input": [ | |
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], | |
"multiplex": { | |
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"LB": "FR05811652", | |
"output": [ | |
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] | |
} | |
} | |
}, | |
{ | |
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"151215_FR05811643_read2_trimmomatic_2PE.fastq.gz" | |
], | |
"multiplex": { | |
"undetermined": { | |
"LB": "FR05811643", | |
"output": [ | |
"FR05811643_trimmed_PE.cram" | |
] | |
} | |
} | |
}, | |
{ | |
"DT": "2015-12-15", | |
"PL": "ILLUMINA", | |
"base input url": "/Users/lg/Desktop/vinu/example/TRIMMED", | |
"input": [ | |
"151215_FR05811643_read1_trimmomatic_1SE.fastq.gz" | |
], | |
"multiplex": { | |
"undetermined": { | |
"LB": "FR05811643", | |
"output": [ | |
"FR05811643_trimmed_SE1.cram" | |
] | |
} | |
} | |
}, | |
{ | |
"DT": "2015-12-15", | |
"PL": "ILLUMINA", | |
"base input url": "/Users/lg/Desktop/vinu/example/TRIMMED", | |
"input": [ | |
"151215_FR05811643_read2_trimmomatic_2SE.fastq.gz" | |
], | |
"multiplex": { | |
"undetermined": { | |
"LB": "FR05811643", | |
"output": [ | |
"FR05811643_trimmed_SE2.cram" | |
] | |
} | |
} | |
}, | |
{ | |
"DT": "2015-12-15", | |
"PL": "ILLUMINA", | |
"base input url": "/Users/lg/Desktop/vinu/example/TRIMMED", | |
"input": [ | |
"151215_FR05811650_read1_trimmomatic_1PE.fastq.gz", | |
"151215_FR05811650_read2_trimmomatic_2PE.fastq.gz" | |
], | |
"multiplex": { | |
"undetermined": { | |
"LB": "FR05811650", | |
"output": [ | |
"FR05811650_trimmed_PE.cram" | |
] | |
} | |
} | |
}, | |
{ | |
"DT": "2015-12-15", | |
"PL": "ILLUMINA", | |
"base input url": "/Users/lg/Desktop/vinu/example/TRIMMED", | |
"input": [ | |
"151215_FR05811650_read1_trimmomatic_1SE.fastq.gz" | |
], | |
"multiplex": { | |
"undetermined": { | |
"LB": "FR05811650", | |
"output": [ | |
"FR05811650_trimmed_SE1.cram" | |
] | |
} | |
} | |
}, | |
{ | |
"DT": "2015-12-15", | |
"PL": "ILLUMINA", | |
"base input url": "/Users/lg/Desktop/vinu/example/TRIMMED", | |
"input": [ | |
"151215_FR05811650_read2_trimmomatic_2SE.fastq.gz" | |
], | |
"multiplex": { | |
"undetermined": { | |
"LB": "FR05811650", | |
"output": [ | |
"FR05811650_trimmed_SE2.cram" | |
] | |
} | |
} | |
}, | |
{ | |
"DT": "2015-12-15", | |
"PL": "ILLUMINA", | |
"base input url": "/Users/lg/Desktop/vinu/example/TRIMMED", | |
"input": [ | |
"151215_FR05811659_read1_trimmomatic_1PE.fastq.gz", | |
"151215_FR05811659_read2_trimmomatic_2PE.fastq.gz" | |
], | |
"multiplex": { | |
"undetermined": { | |
"LB": "FR05811659", | |
"output": [ | |
"FR05811659_trimmed_PE.cram" | |
] | |
} | |
} | |
}, | |
{ | |
"DT": "2015-12-15", | |
"PL": "ILLUMINA", | |
"base input url": "/Users/lg/Desktop/vinu/example/TRIMMED", | |
"input": [ | |
"151215_FR05811659_read1_trimmomatic_1SE.fastq.gz" | |
], | |
"multiplex": { | |
"undetermined": { | |
"LB": "FR05811659", | |
"output": [ | |
"FR05811659_trimmed_SE1.cram" | |
] | |
} | |
} | |
}, | |
{ | |
"DT": "2015-12-15", | |
"PL": "ILLUMINA", | |
"base input url": "/Users/lg/Desktop/vinu/example/TRIMMED", | |
"input": [ | |
"151215_FR05811659_read2_trimmomatic_2SE.fastq.gz" | |
], | |
"multiplex": { | |
"undetermined": { | |
"LB": "FR05811659", | |
"output": [ | |
"FR05811659_trimmed_SE2.cram" | |
] | |
} | |
} | |
}, | |
{ | |
"DT": "2015-12-15", | |
"PL": "ILLUMINA", | |
"base input url": "/Users/lg/Desktop/vinu/example/TRIMMED", | |
"input": [ | |
"151215_FR05811642_read1_trimmomatic_1PE.fastq.gz", | |
"151215_FR05811642_read2_trimmomatic_2PE.fastq.gz" | |
], | |
"multiplex": { | |
"undetermined": { | |
"LB": "FR05811642", | |
"output": [ | |
"FR05811642_trimmed_PE.cram" | |
] | |
} | |
} | |
}, | |
{ | |
"DT": "2015-12-15", | |
"PL": "ILLUMINA", | |
"base input url": "/Users/lg/Desktop/vinu/example/TRIMMED", | |
"input": [ | |
"151215_FR05811642_read1_trimmomatic_1SE.fastq.gz" | |
], | |
"multiplex": { | |
"undetermined": { | |
"LB": "FR05811642", | |
"output": [ | |
"FR05811642_trimmed_SE1.cram" | |
] | |
} | |
} | |
}, | |
{ | |
"DT": "2015-12-15", | |
"PL": "ILLUMINA", | |
"base input url": "/Users/lg/Desktop/vinu/example/TRIMMED", | |
"input": [ | |
"151215_FR05811642_read2_trimmomatic_2SE.fastq.gz" | |
], | |
"multiplex": { | |
"undetermined": { | |
"LB": "FR05811642", | |
"output": [ | |
"FR05811642_trimmed_SE2.cram" | |
] | |
} | |
} | |
}, | |
{ | |
"DT": "2015-12-15", | |
"PL": "ILLUMINA", | |
"base input url": "/Users/lg/Desktop/vinu/example/TRIMMED", | |
"input": [ | |
"151215_FR05811651_read1_trimmomatic_1PE.fastq.gz", | |
"151215_FR05811651_read2_trimmomatic_2PE.fastq.gz" | |
], | |
"multiplex": { | |
"undetermined": { | |
"LB": "FR05811651", | |
"output": [ | |
"FR05811651_trimmed_PE.cram" | |
] | |
} | |
} | |
}, | |
{ | |
"DT": "2015-12-15", | |
"PL": "ILLUMINA", | |
"base input url": "/Users/lg/Desktop/vinu/example/TRIMMED", | |
"input": [ | |
"151215_FR05811651_read1_trimmomatic_1SE.fastq.gz" | |
], | |
"multiplex": { | |
"undetermined": { | |
"LB": "FR05811651", | |
"output": [ | |
"FR05811651_trimmed_SE1.cram" | |
] | |
} | |
} | |
}, | |
{ | |
"DT": "2015-12-15", | |
"PL": "ILLUMINA", | |
"base input url": "/Users/lg/Desktop/vinu/example/TRIMMED", | |
"input": [ | |
"151215_FR05811651_read2_trimmomatic_2SE.fastq.gz" | |
], | |
"multiplex": { | |
"undetermined": { | |
"LB": "FR05811651", | |
"output": [ | |
"FR05811651_trimmed_SE2.cram" | |
] | |
} | |
} | |
}, | |
{ | |
"DT": "2015-12-15", | |
"PL": "ILLUMINA", | |
"base input url": "/Users/lg/Desktop/vinu/example/TRIMMED", | |
"input": [ | |
"151215_FR05811644_read1_trimmomatic_1PE.fastq.gz", | |
"151215_FR05811644_read2_trimmomatic_2PE.fastq.gz" | |
], | |
"multiplex": { | |
"undetermined": { | |
"LB": "FR05811644", | |
"output": [ | |
"FR05811644_trimmed_PE.cram" | |
] | |
} | |
} | |
}, | |
{ | |
"DT": "2015-12-15", | |
"PL": "ILLUMINA", | |
"base input url": "/Users/lg/Desktop/vinu/example/TRIMMED", | |
"input": [ | |
"151215_FR05811644_read1_trimmomatic_1SE.fastq.gz" | |
], | |
"multiplex": { | |
"undetermined": { | |
"LB": "FR05811644", | |
"output": [ | |
"FR05811644_trimmed_SE1.cram" | |
] | |
} | |
} | |
}, | |
{ | |
"DT": "2015-12-15", | |
"PL": "ILLUMINA", | |
"base input url": "/Users/lg/Desktop/vinu/example/TRIMMED", | |
"input": [ | |
"151215_FR05811644_read2_trimmomatic_2SE.fastq.gz" | |
], | |
"multiplex": { | |
"undetermined": { | |
"LB": "FR05811644", | |
"output": [ | |
"FR05811644_trimmed_SE2.cram" | |
] | |
} | |
} | |
}, | |
{ | |
"DT": "2015-12-15", | |
"PL": "ILLUMINA", | |
"base input url": "/Users/lg/Desktop/vinu/example/TRIMMED", | |
"input": [ | |
"151215_FR05811658_read1_trimmomatic_1PE.fastq.gz", | |
"151215_FR05811658_read2_trimmomatic_2PE.fastq.gz" | |
], | |
"multiplex": { | |
"undetermined": { | |
"LB": "FR05811658", | |
"output": [ | |
"FR05811658_trimmed_PE.cram" | |
] | |
} | |
} | |
}, | |
{ | |
"DT": "2015-12-15", | |
"PL": "ILLUMINA", | |
"base input url": "/Users/lg/Desktop/vinu/example/TRIMMED", | |
"input": [ | |
"151215_FR05811658_read1_trimmomatic_1SE.fastq.gz" | |
], | |
"multiplex": { | |
"undetermined": { | |
"LB": "FR05811658", | |
"output": [ | |
"FR05811658_trimmed_SE1.cram" | |
] | |
} | |
} | |
}, | |
{ | |
"DT": "2015-12-15", | |
"PL": "ILLUMINA", | |
"base input url": "/Users/lg/Desktop/vinu/example/TRIMMED", | |
"input": [ | |
"151215_FR05811658_read2_trimmomatic_2SE.fastq.gz" | |
], | |
"multiplex": { | |
"undetermined": { | |
"LB": "FR05811658", | |
"output": [ | |
"FR05811658_trimmed_SE2.cram" | |
] | |
} | |
} | |
} | |
] |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
#!/bin/sh | |
mkdir example; | |
( cd example; | |
touch HJWKJCCXX_2_151215_FR05811676_Homo-sapiens__R_151215_YOUIDA_M001_R1.fastq.gz; | |
touch HJWKJCCXX_2_151215_FR05811676_Homo-sapiens__R_151215_YOUIDA_M001_R2.fastq.gz; | |
touch HJWKJCCXX_3_151215_FR05811682_Homo-sapiens__R_151215_YOUIDA_M001_R1.fastq.gz; | |
touch HJWKJCCXX_3_151215_FR05811682_Homo-sapiens__R_151215_YOUIDA_M001_R2.fastq.gz; | |
touch HJWKJCCXX_4_151215_FR05811683_Homo-sapiens__R_151215_YOUIDA_M001_R1.fastq.gz; | |
touch HJWKJCCXX_4_151215_FR05811683_Homo-sapiens__R_151215_YOUIDA_M001_R2.fastq.gz; | |
touch HJWKJCCXX_5_151215_FR05811684_Homo-sapiens__R_151215_YOUIDA_M001_R1.fastq.gz; | |
touch HJWKJCCXX_5_151215_FR05811684_Homo-sapiens__R_151215_YOUIDA_M001_R2.fastq.gz; | |
touch HK7YCCCXX_4_151215_FR05811634_Homo-sapiens__R_151215_YOUIDA_M001_R1.fastq.gz; | |
touch HK7YCCCXX_4_151215_FR05811634_Homo-sapiens__R_151215_YOUIDA_M001_R2.fastq.gz; | |
touch HK7YCCCXX_5_151215_FR05811650_Homo-sapiens__R_151215_YOUIDA_M001_R1.fastq.gz; | |
touch HK7YCCCXX_5_151215_FR05811650_Homo-sapiens__R_151215_YOUIDA_M001_R2.fastq.gz; | |
touch HKJHJCCXX_1_151215_FR05811674_Homo-sapiens__R_151215_YOUIDA_M001_R1.fastq.gz; | |
touch HKJHJCCXX_1_151215_FR05811674_Homo-sapiens__R_151215_YOUIDA_M001_R2.fastq.gz; | |
touch HKJHJCCXX_2_151215_FR05811652_Homo-sapiens__R_151215_YOUIDA_M001_R1.fastq.gz; | |
touch HKJHJCCXX_2_151215_FR05811652_Homo-sapiens__R_151215_YOUIDA_M001_R2.fastq.gz; | |
touch HKJHJCCXX_3_151215_FR05811658_Homo-sapiens__R_151215_YOUIDA_M001_R1.fastq.gz; | |
touch HKJHJCCXX_3_151215_FR05811658_Homo-sapiens__R_151215_YOUIDA_M001_R2.fastq.gz; | |
touch HKJHJCCXX_4_151215_FR05811659_Homo-sapiens__R_151215_YOUIDA_M001_R1.fastq.gz; | |
touch HKJHJCCXX_4_151215_FR05811659_Homo-sapiens__R_151215_YOUIDA_M001_R2.fastq.gz; | |
touch HKJHJCCXX_5_151215_FR05811660_Homo-sapiens__R_151215_YOUIDA_M001_R1.fastq.gz; | |
touch HKJHJCCXX_5_151215_FR05811660_Homo-sapiens__R_151215_YOUIDA_M001_R2.fastq.gz; | |
touch HKJHJCCXX_6_151215_FR05811666_Homo-sapiens__R_151215_YOUIDA_M001_R1.fastq.gz; | |
touch HKJHJCCXX_6_151215_FR05811666_Homo-sapiens__R_151215_YOUIDA_M001_R2.fastq.gz; | |
touch HKJHJCCXX_7_151215_FR05811667_Homo-sapiens__R_151215_YOUIDA_M001_R1.fastq.gz; | |
touch HKJHJCCXX_7_151215_FR05811667_Homo-sapiens__R_151215_YOUIDA_M001_R2.fastq.gz; | |
touch HKJHJCCXX_8_151215_FR05811668_Homo-sapiens__R_151215_YOUIDA_M001_R1.fastq.gz; | |
touch HKJHJCCXX_8_151215_FR05811668_Homo-sapiens__R_151215_YOUIDA_M001_R2.fastq.gz; | |
touch HKJWVCCXX_4_151215_FR05811651_Homo-sapiens__R_151215_YOUIDA_M001_R1.fastq.gz; | |
touch HKJWVCCXX_4_151215_FR05811651_Homo-sapiens__R_151215_YOUIDA_M001_R2.fastq.gz; | |
touch HKJWVCCXX_5_151215_FR05811636_Homo-sapiens__R_151215_YOUIDA_M001_R1.fastq.gz; | |
touch HKJWVCCXX_5_151215_FR05811636_Homo-sapiens__R_151215_YOUIDA_M001_R2.fastq.gz; | |
touch HKJWVCCXX_6_151215_FR05811642_Homo-sapiens__R_151215_YOUIDA_M001_R1.fastq.gz; | |
touch HKJWVCCXX_6_151215_FR05811642_Homo-sapiens__R_151215_YOUIDA_M001_R2.fastq.gz; | |
touch HKJWVCCXX_7_151215_FR05811643_Homo-sapiens__R_151215_YOUIDA_M001_R1.fastq.gz; | |
touch HKJWVCCXX_7_151215_FR05811643_Homo-sapiens__R_151215_YOUIDA_M001_R2.fastq.gz; | |
touch HKJWVCCXX_8_151215_FR05811644_Homo-sapiens__R_151215_YOUIDA_M001_R1.fastq.gz; | |
touch HKJWVCCXX_8_151215_FR05811644_Homo-sapiens__R_151215_YOUIDA_M001_R2.fastq.gz; | |
touch HKK7VCCXX_5_151215_FR05811635_Homo-sapiens__R_151215_YOUIDA_M001_R1.fastq.gz; | |
touch HKK7VCCXX_5_151215_FR05811635_Homo-sapiens__R_151215_YOUIDA_M001_R2.fastq.gz; | |
touch md5sum_2.txt; | |
touch md5Sum.sh; | |
touch md5sum.txt; | |
touch nohup.out; | |
touch nohup.out.Download2; | |
touch nohup.out.old; | |
touch nohup.out.upload.old; | |
touch pwd.txt; | |
mkdir TRIMMED; | |
( cd TRIMMED; | |
touch 151215_FR05811634_read1_trimmomatic_1PE.fastq.gz | |
touch 151215_FR05811634_read1_trimmomatic_1SE.fastq.gz | |
touch 151215_FR05811634_read2_trimmomatic_2PE.fastq.gz | |
touch 151215_FR05811634_read2_trimmomatic_2SE.fastq.gz | |
touch 151215_FR05811635_read1_trimmomatic_1PE.fastq.gz | |
touch 151215_FR05811635_read1_trimmomatic_1SE.fastq.gz | |
touch 151215_FR05811635_read2_trimmomatic_2PE.fastq.gz | |
touch 151215_FR05811635_read2_trimmomatic_2SE.fastq.gz | |
touch 151215_FR05811636_read1_trimmomatic_1PE.fastq.gz | |
touch 151215_FR05811636_read1_trimmomatic_1SE.fastq.gz | |
touch 151215_FR05811636_read2_trimmomatic_2PE.fastq.gz | |
touch 151215_FR05811636_read2_trimmomatic_2SE.fastq.gz | |
touch 151215_FR05811642_read1_trimmomatic_1PE.fastq.gz | |
touch 151215_FR05811642_read1_trimmomatic_1SE.fastq.gz | |
touch 151215_FR05811642_read2_trimmomatic_2PE.fastq.gz | |
touch 151215_FR05811642_read2_trimmomatic_2SE.fastq.gz | |
touch 151215_FR05811643_read1_trimmomatic_1PE.fastq.gz | |
touch 151215_FR05811643_read1_trimmomatic_1SE.fastq.gz | |
touch 151215_FR05811643_read2_trimmomatic_2PE.fastq.gz | |
touch 151215_FR05811643_read2_trimmomatic_2SE.fastq.gz | |
touch 151215_FR05811644_read1_trimmomatic_1PE.fastq.gz | |
touch 151215_FR05811644_read1_trimmomatic_1SE.fastq.gz | |
touch 151215_FR05811644_read2_trimmomatic_2PE.fastq.gz | |
touch 151215_FR05811644_read2_trimmomatic_2SE.fastq.gz | |
touch 151215_FR05811650_read1_trimmomatic_1PE.fastq.gz | |
touch 151215_FR05811650_read1_trimmomatic_1SE.fastq.gz | |
touch 151215_FR05811650_read2_trimmomatic_2PE.fastq.gz | |
touch 151215_FR05811650_read2_trimmomatic_2SE.fastq.gz | |
touch 151215_FR05811651_read1_trimmomatic_1PE.fastq.gz | |
touch 151215_FR05811651_read1_trimmomatic_1SE.fastq.gz | |
touch 151215_FR05811651_read2_trimmomatic_2PE.fastq.gz | |
touch 151215_FR05811651_read2_trimmomatic_2SE.fastq.gz | |
touch 151215_FR05811652_read1_trimmomatic_1PE.fastq.gz | |
touch 151215_FR05811652_read1_trimmomatic_1SE.fastq.gz | |
touch 151215_FR05811652_read2_trimmomatic_2PE.fastq.gz | |
touch 151215_FR05811652_read2_trimmomatic_2SE.fastq.gz | |
touch 151215_FR05811658_read1_trimmomatic_1PE.fastq.gz | |
touch 151215_FR05811658_read1_trimmomatic_1SE.fastq.gz | |
touch 151215_FR05811658_read2_trimmomatic_2PE.fastq.gz | |
touch 151215_FR05811658_read2_trimmomatic_2SE.fastq.gz | |
touch 151215_FR05811659_read1_trimmomatic_1PE.fastq.gz | |
touch 151215_FR05811659_read1_trimmomatic_1SE.fastq.gz | |
touch 151215_FR05811659_read2_trimmomatic_2PE.fastq.gz | |
touch 151215_FR05811659_read2_trimmomatic_2SE.fastq.gz | |
touch 151215_FR05811660_read1_trimmomatic_1PE.fastq.gz | |
touch 151215_FR05811660_read1_trimmomatic_1SE.fastq.gz | |
touch 151215_FR05811660_read2_trimmomatic_2PE.fastq.gz | |
touch 151215_FR05811660_read2_trimmomatic_2SE.fastq.gz | |
touch 151215_FR05811666_read1_trimmomatic_1PE.fastq.gz | |
touch 151215_FR05811666_read1_trimmomatic_1SE.fastq.gz | |
touch 151215_FR05811666_read2_trimmomatic_2PE.fastq.gz | |
touch 151215_FR05811666_read2_trimmomatic_2SE.fastq.gz | |
touch 151215_FR05811667_read1_trimmomatic_1PE.fastq.gz | |
touch 151215_FR05811667_read1_trimmomatic_1SE.fastq.gz | |
touch 151215_FR05811667_read2_trimmomatic_2PE.fastq.gz | |
touch 151215_FR05811667_read2_trimmomatic_2SE.fastq.gz | |
touch 151215_FR05811668_read1_trimmomatic_1PE.fastq.gz | |
touch 151215_FR05811668_read1_trimmomatic_1SE.fastq.gz | |
touch 151215_FR05811668_read2_trimmomatic_2PE.fastq.gz | |
touch 151215_FR05811668_read2_trimmomatic_2SE.fastq.gz | |
touch 151215_FR05811674_read1_trimmomatic_1PE.fastq.gz | |
touch 151215_FR05811674_read1_trimmomatic_1SE.fastq.gz | |
touch 151215_FR05811674_read2_trimmomatic_2PE.fastq.gz | |
touch 151215_FR05811674_read2_trimmomatic_2SE.fastq.gz | |
touch 151215_FR05811676_read1_trimmomatic_1PE.fastq.gz | |
touch 151215_FR05811676_read1_trimmomatic_1SE.fastq.gz | |
touch 151215_FR05811676_read2_trimmomatic_2PE.fastq.gz | |
touch 151215_FR05811676_read2_trimmomatic_2SE.fastq.gz | |
touch 151215_FR05811682_read1_trimmomatic_1PE.fastq.gz | |
touch 151215_FR05811682_read1_trimmomatic_1SE.fastq.gz | |
touch 151215_FR05811682_read2_trimmomatic_2PE.fastq.gz | |
touch 151215_FR05811682_read2_trimmomatic_2SE.fastq.gz | |
touch 151215_FR05811683_read1_trimmomatic_1PE.fastq.gz | |
touch 151215_FR05811683_read1_trimmomatic_1SE.fastq.gz | |
touch 151215_FR05811683_read2_trimmomatic_2PE.fastq.gz | |
touch 151215_FR05811683_read2_trimmomatic_2SE.fastq.gz | |
touch 151215_FR05811684_read1_trimmomatic_1PE.fastq.gz | |
touch 151215_FR05811684_read1_trimmomatic_1SE.fastq.gz | |
touch 151215_FR05811684_read2_trimmomatic_2PE.fastq.gz | |
touch 151215_FR05811684_read2_trimmomatic_2SE.fastq.gz | |
touch nohup.out; | |
); | |
); |
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